Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia

H5N1 highly pathogenic avian influenza (HPAI) viruses have seriously affected the Asian poultry industry since their recurrence in 2003. The viruses pose a threat of emergence of a global pandemic influenza through point mutation or reassortment leading to a strain that can effectively transmit among humans. In this study, we present phylogenetic evidences for the interlineage reassortment among H5N1 HPAI viruses isolated from humans, cats, and birds in Indonesia, and identify the potential genetic parents of the reassorted genome segments. Parsimony analyses of viral phylogeography suggest that the reassortant viruses may have originated from greater Jakarta and surroundings, and subsequently spread to other regions in the West Java province. In addition, Bayesian methods were used to elucidate the genetic diversity dynamics of the reassortant strain and one of its genetic parents, which revealed a more rapid initial growth of genetic diversity in the reassortant viruses relative to their genetic parent. These results demonstrate that interlineage exchange of genetic information may play a pivotal role in determining viral genetic diversity in a focal population. Moreover, our study also revealed significantly stronger diversifying selection on the M1 and PB2 genes in the lineages preceding and subsequent to the emergence of the reassortant viruses, respectively. We discuss how the corresponding mutations might drive the adaptation and onward transmission of the newly formed reassortant viruses

The effect of low temperature and low light intensity on nutrient removal from municipal wastewater by purple phototrophic bacteria (PPB)

There has been increased interest in alternative wastewater treatment systems to improve nutrient recovery while achieving acceptable TCOD, TN, and TP discharge limits. Purple phototrophic bacteria (PPB) have a high potential for simultaneous nutrient removal and recovery from wastewater. This study evaluated the PPB performance and its growth at different operating conditions with a focus on HRT and light optimization using a continuous-flow membrane photobioreactor (PHB). Furthermore, the effect of low temperature on PPB performance was assessed to evaluate the PPB’s application in cold-climate regions. In order to evaluate PPB performance, TCOD, TN, and TP removal efficiencies and Monod kinetic parameters were analyzed at different HRTs (36, 18, and 9 h), at temperatures of 22°C and 11°C and infrared (IR) light intensities of 50, 3, and 1.4 Wm-2. The results indicated that low temperature had no detrimental impact on PPB’s performance. The photobioreactor (PHB) with cold-enriched PPB has a high potential to treat municipal wastewater with effluent concentrations below target limits (TCOD˂ 50mgL-1, TN˂10 mgL-1, and TP˂1 mgL-1). Monod kinetic parameters Ks, K, Y, and Kd were estimated at 20-29 mgCODL-1, 1.6-1.9 mgCOD(mgVSS.d)-1, 0.47 mgVSS mgCOD-1, and 0.07-0.08 d-1 at temperatures of 11°C-22°C respectively. The results of the steady-state mass balances showed TCOD, TN, and TP recoveries of 80%-86%, which reflected PPB’s substrate and nutrient assimilation. Previous studies utilized high light intensities (˃ 50 Wm-2) to provide PPB with the maximum energy required for its growth. In order to enable the PPB technology as a practical approach in municipal wastewater treatment, light intensity must be optimized. Based on the literature, there is no study on PPB performance at low light intensities using a continuous-flow membrane photobioreactor. The effect of low light intensities of 3, and 1.4 Wm-2 on PPB performance was addressed in this study. The results indicated that PPB at a light intensity as low as 1.4 Wm-2 were able to treat municipal wastewater with effluent concentrations below above-mentioned target limits. Light intensity (1-50 Wm-2) had no detrimental impact on PPB performance and Monod kinetic parameters. This study showed that the optimized light intensity required for municipal wastewater treatment with PPB is significantly lower than previously indicated in the literature. The energy consumptions attributed to PHB’s illumination of 3, and 1.4 Wm-2 were determined to be 1.44, and 0.67 kWh/m3 which is significantly lower than previous studies (˃ 24 kWh/m3)

MicroRNA degradation by a conserved target RNA regulates animal behavior

International audiencemicroRNAs (miRNAs) repress target transcripts through partial complementarity. By contrast, highly complementary miRNA-binding sites within viral and artificially engineered transcripts induce miRNA degradation in vitro and in cell lines. Here, we show that a genome-encoded transcript harboring a near-perfect and deeply conserved miRNA-binding site for miR-29 controls zebrafish and mouse behavior. This transcript originated in basal vertebrates as a long noncoding RNA (lncRNA) and evolved to the protein-coding gene NREP in mammals, where the miR-29-binding site is located within the 3′ UTR. We show that the near-perfect miRNA site selectively triggers miR-29b destabilization through 3′ trimming and restricts its spatial expression in the cerebellum. Genetic disruption of the miR-29 site within mouse Nrep results in ectopic expression of cerebellar miR-29b and impaired coordination and motor learning. Thus, we demonstrate an endogenous target-RNA-directed miRNA degradation event and its requirement for animal behavio

The genomic and epidemiological dynamics of human influenza A virus

The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions